Rv1700 Resolved · high auto-curated
H37Rv Rv1700 · MTBC0 mtbc0_001808 ·
207 aa · 1937597–1938220 (+) ·
RefSeq NP_216216.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | NUDIX hydrolase |
|---|---|
| MTBC0 PGAP re-annotation | ADP-ribose diphosphatase |
| Revised (this work) | ADP-ribose diphosphatase. Pfam: NDPSase_N (PF28549.1), NUDIX (PF00293.35). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X235
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ADP-ribose pyrophosphatase |
| EC (curated) |
EC 3.6.1.13, EC 3.6.1.58
|
| Curated function | Catalyzes the hydrolysis of ADP-ribose (ADPR) to AMP and ribose-5-phosphate. Can also hydrolyze ADP-mannose and ADP-glucose, with lower efficiency. Has weaker activity with NAD, GDP-sugars and UDP-sugars. Also catalyzes the conversion of 8-oxo-dGDP to 8-oxo-dGMP, and 8-oxo-GDP to 8-oxo-GMP. Functions in concert with MutT1 to detoxify 8-oxo-dGTP to 8-oxo-dGMP and may play an important role in supporting cellular growth under oxidative stress. The catalytic efficiency is much higher for the hydrolysis of ADPR than 8-oxo-dGTP, suggesting a more relevant biological role in hydrolysis of ADPR. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | nudF |
| eggNOG description | pfam nudix |
| Orthologous group | COG0494 |
| EC number |
EC 3.6.1.13
|
| KEGG orthology |
K01515
|
| KEGG pathways |
map00230
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 1.724 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
NDPSase_N | PF28549.1 | 2.9e-09 | 7–40 | Nucleoside diphosphate sugar hydrolase N-terminal domain |
NUDIX | PF00293.35 | 1.8e-13 | 44–156 | NUDIX domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pyrG (CTP synthase), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1699 pyrG |
CTP synthase | 996 | 983 ctx | neighborhood:882 coexpression:862 textmining:817 |
Rv1701 xerD |
tyrosine recombinase XerD | 996 | 976 ctx | neighborhood:882 coexpression:801 textmining:870 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 952 | 946 | experimental:787 database:643 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 784 | 771 | experimental:403 database:615 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 782 | 769 | experimental:403 database:615 |
Rv1698 mctB |
copper transporter MctB | 757 | 758 ctx | neighborhood:754 |
Rv1697 steA hyp |
hypothetical protein | 736 | 736 ctx | neighborhood:733 |
Rv2524c fas |
fatty acid synthase | 675 | 663 | database:406 |
Rv1694 tlyA |
16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA | 657 | 657 ctx | neighborhood:648 |
Rv1340 rphA |
ribonuclease PH | 683 | 653 | database:636 |
Rv1695 ppnK |
inorganic polyphosphate/ATP-NAD kinase | 671 | 653 ctx | neighborhood:648 |
Rv1691 hyp |
hypothetical protein | 656 | 644 ctx | neighborhood:451 |
Rv3339c icd1 |
isocitrate dehydrogenase | 597 | 597 | database:581 |
Rv2985 mutT1 |
8-oxo-dGTP diphosphatase | 609 | 582 | database:500 |
Rv1391 dfp |
bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase | 580 | 581 | database:556 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: NUDIX hydrolase
- MTBC0 PGAP product: ADP-ribose diphosphatase
- Pfam (hmmscan --cut_ga): NDPSase_N PF28549.1 (E=3e-09), NUDIX PF00293.35 (E=2e-13)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_216216.1)
- Domains: Pfam-A via hmmscan --cut_ga — NDPSase_N (PF28549.1), NUDIX (PF00293.35)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0494 - Curated reference: UniProt I6X235 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
101 functional partner(s); context anchor
pyrG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001808|Rv1700| MAEHDFETISSETLHTGAIFALRRDQVRMPGGGIVTREVVEHFGAVAIVAMDDNGNIPMVYQYRHTYGRRLWELPAGLLDVAGEPPHLTAARELREEVGLQASTWQVLVDLDTAPGFSDESVRVYLATGLREVGRPEAHHEEADMTMGWYPIAEAARRVLRGEIVNSIAIAGVLAVHAVTTGFAQPRPLDTEWIDRPTAFAARRAER